The issue with the 3DS is anti-piracy technology. The format hasn't been cracked yet as well. We'll get there, though. Even Starforce which was a pain to crack was eventually cracked, although it was when people had already lost all interest in Starforce-protected games, and after most publishers moved away from Starforce due to the potential harm it caused to people's PCs.
The fact it's 3D has nothing to do with cracking difficulty. The N64 was full 3D and was cracked.
It seems that, with the 3DS, Nintendo are really trying to make life difficult for hackers. Cheap flashcarts are permanently blocked. 3DS roms still aren't available (I'm sure they exist but they're useless right now). Heck, when Ruby and Sapphire were released I was playing the US version of Ruby on VBA almost on day one since release. Meanwhile, X and Y will come out in September(?) this year and you can bet there will be no 3DS emulators nor flashcarts on the day of their release.
I think the best way Nintendo can fight piracy is to make X and Y available as digital downloads through their store. Of course many people prefer boxed but a Steam-like service is one of the most efficient ways to fight piracy. It would kill flashcarts and put a huge dent on emulator play. Emulators as means of piracy are already unfavored because you can't access Wi-Fi with Desmume which is the best one available. Actually you can, with an obscure build, but from what I heard the Pokémon servers already block it. The idea of providing a complete service in one digital package would make people flock to Nintendo's shop and shy away from emulators and flashcarts.
People always find ways to go around stuff like that, especially with something popular like Pokemon.
Desmume Wi-Fi works and it isn't blocked by Pokemon servers.
Hackers have already found a way to exploit the 3DS not too long ago. They're not very far from having flashcarts made.
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